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Article ID: WMC003159 ISSN 2046-1690

Is Your Journal Indexed in PubMed? Relevance of PubMed in Biomedical Today

Corresponding Author: Mr. Kamal K Mahawar, Consultant Surgeon, City Hospitals Sunderland NHS Trust, Sunderland - United Kingdom

Submitting Author: Dr. Deepak Kejariwal, Consultant Gastroenterologist, University Hospital of North Durham - United Kingdom

Article ID: WMC003159 Article Type: Review articles Submitted on:17-Mar-2012, 05:12:39 AM GMT Published on: 17-Mar-2012, 07:16:40 AM GMT Article URL: http://www.webmedcentral.com/article_view/3159 Subject Categories:MISCELLANEOUS Keywords:Literature, PubMed, Bibliographic , , How to cite the article:Kejariwal D, Mahawar KK. Is Your Journal Indexed in PubMed? Relevance of PubMed in Biomedical Scientific Literature Today . WebmedCentral MISCELLANEOUS 2012;3(3):WMC003159 : This is an open-access article distributed under the terms of the Attribution License, which permits unrestricted use, distribution, and in any medium, provided the original author and source are credited. Source(s) of Funding: None. Authors have used their personal time to write this article.

Competing Interests: Webmed Limited, UK owns the portal WebmedCentral. DK is its chairman and KM is its CEO. Both are shareholders and directors in the company.

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Is Your Journal Indexed in PubMed? Relevance of PubMed in Biomedical Scientific Literature Today

Author(s): Kejariwal D, Mahawar KK

Introduction should have sophisticated features to track and analyse f. Free: Ideally, such a resource should be completely free for users along with free access to full text articles. The arrival and spread of internet has enabled of better bibliographic scientific We discuss here briefly the major scientific databases databases with significantly improved capacity for available currently, their background, and their storage and retrieval. In recent years, electronic important characteristics. We also examine how they database searching has become the default mode of fair against the criteria above. bio-medical information retrieval. The National of (NLM) in the United States introduced the Important Databases first interactive searchable database (Medline) in 1971. Subsequently, in 1996, it added the “Old Medline” database with coverage of publications between 1950 PubMed: and 1965. In 1997, NLM launched PubMed (a Advent of PubMed was a major landmark in history of combination of both Old Medline and Medline) (1). electronic archiving of biomedical scientific literature. It Several other databases have emerged over the last is a free resource that is developed and maintained by two decades, each tackling the issue from a slightly NCBI (National Center for Biotechnology Information) different angle. Here, we examine these databases at the NLM (National Library of Medicine), at US against our criteria for an ideal database and suggest National Institute of Health (NIH) (2). It comprises over areas for further improvement. 21 million citations from biomedical literature from Characteristics of an Ideal MEDLINE (a huge database of over 19 million references to articles published in approximately 5,600 current biomedical journals from the United States and over 80 foreign countries), some additional journals(not indexed in Since these databases are so important for MEDLINE), and online (2). As of November information storage and retrieval, it is crucial that we 2011, 5,582 journals were indexed with MEDLINE (3). have scientific databases fit for purpose. In our opinion, a scientific database should ideally have PubMed citations and abstracts include the fields of following characteristics. biomedicine and health, covering portions of the life , behavioral sciences, chemical sciences, and a. Inclusive: It should cover all scientific and bioengineering. PubMed also provides access to must not exclude any piece of research. Ideally, it additional relevant web sites and links to the other should also include non peer reviewed (for example NCBI molecular resource (2). Publishers of , conference papers, webpage/blogs journals can submit their citations to NCBI. If the etc) information, the so called “gray literature”. publisher has a web site that offers full-text of its b. Specific Refined Search: At the same time, it journals, PubMed provides links to that site as well as should bring out the most relevant information to a biological resources, consumer health information, user. research tools, and more. c. Advanced Filters: It should have a variety of filters Criteria for inclusion of a journal into MEDLINE (4) for specialty, dates, keywords, peer reviewed/non peer (and hence into PubMed) can seem arbitrary. There is reviewed, blogs, geographical location etc for an ideal no single criterion which is crucial and they seem to be user experience. using a number of them to determine the suitability of d. Link to Full text articles: It should provide link to full journal. Even though it is widely held that PubMed will text articles. Print only journals need to be encouraged only consider Peer Reviewed literature (5), they to look for ways for electronically archiving their work. explicitly state on their website that this is not the case, e. Advanced : An ideal database “Most journals in PubMed are peer-reviewed or

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refereed. Non-editorial journal-staff review original engine. Even before the advent of Google Scholar and articles before the articles are accepted for publication. also today, many years after it, a large number of Criteria for and the qualifications of peers academicians rely on simple Google search to look for or referees vary among publishers. We have no list of scientific content. However, the search on Google, peer-reviewed/refereed journals in PubMed; and you looking for academic content, can be very frustrating cannot limit your search to peer-reviewed journals with popular websites, promotional content and blogs using PubMed” (6). Overall 20-25% of titles reviewed competing with scholarly content written by are selected for indexing with MEDLINE. for a scientific audience. Users have no way of PubMed stands out as a bibliographic database for knowing how to interpret relative merit of search biomedical scientists. It has much to recommend itself. results. Google Scholar would seem like an attempt It has been successful in encouraging a large number from Google to make this search more specific and of publishers to work with it and its user is relevant for academic community. constantly growing. It is totally free to use and It obtains its information directly from publishers and provides free abstracts. Its filters are reasonably good. by crawling the web for scholarly content. It searches It links out to full text articles and, with the help of for scholarly such as peer-reviewed papers, PubMed Central, is building a great resource of free theses, books, , abstracts and technical full text articles. However, it excludes a large body of reports from broad areas of research. Google Scholar both peer reviewed and also the so called “gray” searches a variety of undisclosed academic publishers, literature (non peer reviewed). Both are significant professional societies, repositories and sources of knowledge, we should make better use of. universities, as well as scholarly articles. Its search Peer Reviewed literature (that has undergone pre results will hence include a variety of peer reviewed publication peer review) has its own limitations (7), scholarly content but also include non peer reviewed that gray literature is free from. Gray literature does scholarly content. There is no clear way of identifying not suffer from any form of , is instant, only peer reviewed content. There has been some and guarantees true freedom of expression to criticism that all the content it shows may not be scientists with contrarian views. Conn et al (8) noted scholarly either. Moreover there seems to be some that meta-analyses that exclude gray literature likely secrecy about what it covers. Google Scholar does not over-represent studies with statistically significant publish a list of scientific journals crawled, and the findings. As early as 2004, Banks had noted that the frequency of its updates is unknown. It is therefore bigger challenge would be to develop bibliographic impossible to know how current or exhaustive resources for gray literature (9). Others (10) have tried searches are in Google Scholar. to develop models to facilitate this. However, by and The exact ranking algorithm used by Google Scholar large, this challenge persists for all of us in 2012. is undisclosed. According to them, “It ranks documents Literature published in a climate of post publication the way researchers do, weighing the full text of each peer review, as on WebmedCentral (11), is a further document, where it was published, who it was written subset of scientific literature that aims to combine best by, as well as how often and how recently it has been of both the worlds of peer reviewed literature and gray cited in other scholarly literature” (14). It is suspected literature. This model of has some support that citation count is probably the most important of (12) and other commercial players are keen to venture several factors it takes into account (15). Google into the foray (13). PubMed will need to find ways to Scholar allows . It may be vulnerable include these too. If it does not, it risks losing some of to spam (16). Use of Google Scholar is free and many its relevance in future. articles are freely available full text. In other cases, it By virtue of its size, PubMed has a dominant position will take you to full text article on publishers’ website. It in the field. Because of its dominant position, journals provides single interface to access library catalogues not considered suitable by PubMed are at an obvious indexes and websites and is relatively easy to use and disadvantage compared to their PubMed included navigate. counterparts. One could argue that by excluding a To some extent, it suffers from the same drawbacks large section of academic literature, PubMed is also that Google search engine does. Users cannot clearly putting science and scientists at a disadvantage. make out what is peer reviewed and what is not; what Google Scholar: is scholarly and what is not. The search results are less cluttered than Google search engine as it Launched in beta version in 2004, it is a Google® excludes the large body of supposedly non scholarly product, company with world’s best internet search information out there. But that also makes it less

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sensitive than Google search engine and perhaps less based. attractive, if one is looking for a relatively rare topic. At the same time, coverage is unclear and incomplete. Discussion Moreover, it is not always scholarly either. Because of the secrecy involved with regards to what it includes and how it ranks information, it is not widely regarded There are many bibliographic databases out there but by biomedical scientists. Google says that MEDLINE none of them perform well against all of the criteria laid citations are a part of Google Scholar but it does not out by us above. PubMed and Embase focus mainly always stand to independent verification. It does on medicine and biomedical sciences, whereas however complement a researcher’s needs by , , and Google Scholar cover covering resources not covered by other citation most scientific fields. PubMed and Google Scholar are indexing bodies. Citation tracking is an advantage and free to use whereas Embase, Scopus and Web of it is free to users. It would seem as if Google Scholar Science are databases that belong to commercial is currently struggling to find its niche but does have a providers and require an access fee. PubMed and significant role to play in free search for scholarly Google Scholar are the only free ones and hence have content. It is bound to improve with time and could been discussed in some depth above. However, the threaten commercial citation tracking databases. selection criteria and the journals indexed for all databases are unclear. All of these databases Scopus: discussed above include non peer reviewed literature It is a bibliographic database (17) containing abstracts despite the widely held view to the contrary. Further. and citations for articles. It covers None of the databases are all inclusive. nearly 18,000 titles from over 5,000 international Some databases often use Bradford’s law (20) to publishers, including coverage of 16,500 justify their non inclusion of all scientific journals. peer-reviewed journals in the scientific, technical, Bradford’s law states that relatively small numbers of medical, and social sciences (including arts and journals publish the bulk of significant scientific results. humanities). The only criteria it mentions for inclusion Hence, in pre electronic era, the law was used to in the database are ISSN number and economically plan information systems and library ‘scholarly/academic’ publication. It is owned by services (21). This is clearly not relevant with the Elsevier and is available online by subscription. It arrival of electronic databases where the costs of allows citation analysis. including all scientific literature would not be Web of science: prohibitive and good search functionality would sort It is provided by Thomson Reuters (18). It covers out the literature in a variety of filters. Bradford’s 11,261 journals (as of September 5, 2009) spanning analysis of choosing journals for databases has also multiple academic disciplines including the sciences, been criticised for not being objective and neutral (22). social sciences, arts, and humanities, and across Further, Bradford law or selectivity in databases disciplines. Web of Science does not cover all journals, clearly tends to favour dominant and views and its coverage in some fields is less complete than while suppressing views other than the mainstream. in others. Web of science mention multiple criteria for As a result of this selectivity, scientists have felt under inclusion in its database. However peer review as a pressure to publish in the best journals, and minimum criterion is not mentioned on its website. It universities to ensure access to that core set of includes non peer reviewed literature like seminars, journals. There is clearly a danger of only representing symposia, conference proceedings etc. Web of majority views if journals are selected in this fashion. Science does not provide any data regarding open In this day and age, with the available technology, it access articles that it includes (if any). It is fee based should be possible for databases to include everything and allows citation analysis. in their fold and identify them by giving them appropriate labels so that users can differentiate Embase: between sources of information. It is a commercial abstracts and index database PubMed is the most used biomedical bibliographic maintained by Elsevier (19). It includes all MEDLINE database. However it excludes a significant body of records produced by the National Library of Medicine literature that diminishes its usefulness. Academicians (NLM), as well as over 5 million records not covered are increasingly using multiple databases to provide a on MEDLINE (over 2,000 currently indexed Embase more inclusive information search. Google scholar is journals are unique). Journals indexed in Embase are the only free creditable option at present apart from mostly peer reviewed. Use of Embase is subscription PubMed. Google is easier to use compared to

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PubMed, which many users find tedious even with all 11/03/2012 its help tutorials (23). Internet search is improving 3. http://www.nlm.nih.gov/bsd/num_titles.html Last everyday and also pulls out the relevant PubMed accessed on 11/03/2012 results. However, it may be too sensitive (24-25). In 4. http://www.nlm.nih.gov/pubs/factsheets/jsel.html 2007, Shultz (26) examined PubMed and Google Last accessed on 11/03/2012 Scholar and found the two complementary. 5. It should be possible for PubMed to include all http://www.fmhs.uaeu.ac.ae/FMHSWEBUserFiles/file/ scholarly content and identify them with appropriate Scholarly%20Peer%20Reviewed%20Journals(1).pptx tags. For example PubMed content that has not Last accessed on 11/03/2012 undergone any peer review could be clearly identified. 6. http://www.nlm.nih.gov/services/peerrev.html Last Bodies like PubMed can reduce the dominance of accessed on 11/03/2012 selected players and themselves become more useful 7. Mahawar KK. Role of Peer Review in Biomedical for scientists in the process. Not surprisingly, scientists Publishing. WebmedCentral MISCELLANEOUS 2011; are looking elsewhere to find literature not covered by 2(4): WMC001863. Last accessed on 11/03/2012 PubMed (27). This has led to development of multiple 8. Conn VS, Valentine JC, Cooper HM, Rantz MJ. commercial databases listed above. PubMed however Gray literature in meta-analyses. Nurs Res 2003; remains an important resource for clinicians and 52(4): 256-61. researchers (28). 9. Banks M. Connections between publishing and access to gray literature. J Med Libr In summary, none of the above databases include all Assoc 2004; 92(2): 164–166. scholarly content and their selection criteria are not 10. Turner AM, Liddy Ed, Bradley J, Wheatley JA . completely obvious. They all include non peer Modelling public health interventions for improved reviewed literature and many are subscription based. access to the gray literature. J Med Libr Assoc 2005; Conclusion 93(4): 487–494. 11. http://www.webmedcentral.com/ Last accessed on 11/03/2012 12. Smith . Classical peer review: an empty gun. There is a need to develop better scientific databases Breast Res. 2010; 12(Suppl 4): S13. for improved storage and retrieval of biomedical 13. http://f1000research.com/ Last accessed on scientific content. It will lead to an improved user 11/03/2012 search experience and quality. PubMed currently 14. http://scholar.google.com/intl/en/scholar/about.html maintains a dominant position in the field but risks Last accessed on 11/03/2012 losing it if it does not keep pace with time. It will need 15. Beel J, Gipp B. Google Scholar’s Ranking to evolve and become more inclusive in future to stay Algorithm: An Introductory Overview. In Birger Larsen ahead in the game. Biomedical scientists need a and Jacqueline Leta, editors, Proceedings of the 12th bibliographic database that will archive all scientific International Conference on and content, identify them with appropriate tags, and is Informetrics (ISSI’09), volume 1, pages 230–241, Rio free to use. de Janeiro (Brazil), July 2009. International Society for Abbreviations Scientometrics and Informetrics. ISSN 2175-1935. Preprint downloaded from http://www.sciplore.org/publications/2009-Google_Sch NCBI: National Center for Biotechnology Information olar%27s_Ranking_Algorithm_--_An_Introductory_Ov NLM: National Library of Medicine erview_--_preprint.pdf. Last accessed on 11/03/2012 NIH: National Institute of Health 16. Joeran Beel and Bela Gipp. On the Robustness of Google Scholar Against Spam. In Proceedings of the References 21th ACM Conference on Hyptertext and Hypermedia. ACM, June 2010 Pre print pdf downloaded from http://www.sciplore.org/publications/2010-On_the_Rob 1. PubMed Overview. ustness_of_Google_Scholar_against_Spam--preprint. http://www.ncbi.nlm.nih.gov/corehtml/query/static/over pdf Last accessed on 11/03/2012 view.html Last accessed on 11/03/2012 17. http://www.scopus.com/home.url Last accessed on 2. 11/03/2012 http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmed 18. help.PubMed_Quick_Start Last accessed on http://thomsonreuters.com/products_services/science/

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science_products/a-z/web_of_science/ Last accessed on 11/03/2012 19. http://www.embase.com/info/what-embase Last accessed on 11/03/2012 20. http://thomsonreuters.com/products_services/science/f ree/essays/journal_selection_process/ Last accessed on 11/03/2012 21. Brookes BC. Bradford’s law and the bibliography of science. 1969; 224: 953-6. 22. Nicolaisen J, Hjørland B. Practical potentials of Bradford's law: a critical examination of the received view. Journal of Documentation 2007; 63 (3): 359 – 377 23. http://laikaspoetnik.wordpress.com/2008/06/11/pubme d-past-present-and-future-part-i/ Last accessed on 11/03/2012 24. Freeman MK, Lauderdale SA, Kendrach MG, Woolley TW. Google Scholar versus PubMed in locating primary literature to answer drug-related questions. Ann Pharmacother 2009; 43(3): 478-84. 25. Anders ME, Evans DP. Comparison of PubMed and Google Scholar literature searches. Respir Care 2010 May; 55(5): 578-83. 26. Shultz M. Comparing test searches in PubMed and Google Scholar. J Med Libr Assoc. 2007 October; 95(4): 442–445. 27. Hendersen J. Google Scholar: A source for clinicians? CMAJ. 2005 June 7; 172(12): 1549–1550. 28. Falagas ME, Pitsouni EI, Malietzis GA, Pappas G. Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses. FASEB J 2008 Feb; 22(2): 338-42.

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